AllonKleinLab / snakemake_QC

Introduction

A snakemake pipeline to perform fastqc and then multi-qc for multiple files on o2!

You can specify the config.yaml files for the analysis. See the test folder for an example project

The config.yaml has the following structure:

script_dir: '../source' # relative or absolute path to the source files
raw_data_dir: 'raw_data' # absolute dir or the relative to the config file
path_format: 0 # format=0, the file is like {raw_data_dir}/{sample}/{sample}.fastq.gz;  
          # format=1, the file is like  {raw_data_dir}/{sample}.fastq.gz
SampleList: ['test_DNA_Lime','test_LARRY_10X']  # sample files to run
sbatch : 1 # 1, run sbatch job;  
           # 0, run in the interactive mode. 
QC:
    max_run_time : 3 # used only if sbatch=1
    requested_memory : '10G' # used only if sbatch=1
    cores: 2
recompute : 0

You can go to the test module and run this following command to execute (before you do, please check that the script_dir is correct in your local machine)

 snakemake   -s path/to/snakefile_QC.py --configfile config.yaml  --cores 4